Chapter 1: A Preview of Cell Biology PDF

Name Rich Milton R. Dulay, PhD, RMicro, DPAM Rank Professor IV Designation Head, CTMRD; Co-Chair, IACUC; Program Leader, Tuklas Lunas Program Education PhD Biology, DLSU-Manila, 2019-2021 MS Biology, DLSU-Manila, 2009-2011 BS Biology...

Name Rich Milton R. Dulay, PhD, RMicro, DPAM Rank Professor IV Designation Head, CTMRD; Co-Chair, IACUC; Program Leader, Tuklas Lunas Program Education PhD Biology, DLSU-Manila, 2019-2021 MS Biology, DLSU-Manila, 2009-2011 BS Biology (Microbiology), CLSU, 2003-2007 Research National Center for Agricultural Utilization Research, Fellowship United States Department of Agriculture, 1815 N. University St., Peoria, Illinois 61604, USA. Research 150 Published Articles in Scopus and WOS journals Credentials 14 Utility Model Applications; 1207 Citations in Goggle Scholar; Hirsh Index = 19 On-going Tuklas Lunas Program, JIRCAS Project, NAST Project, Project ARC Projects Award 2022 NAST Outstanding Young Scientist Central Luzon State University 1. Vision of the University Central Luzon State University (CLSU) as a world-class National University for science and technology in agriculture and allied fields. 2. Mission of the University CLSU shall develop globally competitive, work-ready, socially-responsible and empowered human resources who value life-long learning; and to generate, disseminate, and apply knowledge and technologies for poverty alleviation, environmental protection, and sustainable development. 3. Educational Philosophy The Central Luzon State University is committed and dedicated to provide a holistic transformative education anchored on its mission statement and its institutional core values. As stated on its mission, the University shall develop globally competitive, work-ready, socially- responsible and empowered human resources who value life-long learning; and shall generate, disseminate, and apply knowledge and technologies for poverty alleviation, environmental protection and sustainable development. In consonance, the educational philosophy of the University is reflective of its teaching and learning environment. Central Luzon State University 4. Quality Policy Statement 1. Excellent service to humanity is our commitment. 2. We are committed to develop globally-competent and empowered human resources, and to generate knowledge and technologies for inclusive societal development. 3. We are dedicated to uphold CLSU’s core values and principles, comply with statutory and regulatory standards and continuously improve the effectiveness of our quality management systems. 4. Mahalaga ang inyong tinig upang higit na mapahusay ang kalidad ng aming paglilingkod.  The Cell Theory: A Brief History The Emergence of Modern Cell Biology Experimental and Model Organism in Modern Cell Biology Research The biological world is a world of cells. Cell biology's origins trace back over 300 years. European scientists pioneered early microscopes for biological exploration. Diverse biological specimens, from bark to bacteria to human sperm, were examined. The cell theory was developed through the work of many different scientists Robert Hooke and Cork Cells: In 1665, Hooke created a microscope. Explored thin slices of cork. Observed and illustrated a network of small compartments resembling honeycomb. Coined the term "cells" (from Latin "cellula" meaning "little room"). The compartments were actually formed by cell walls of dead plant tissue (cork). Hooke's lack of understanding regarding their vitality. Leeuwenhoek (magnification power) became the BROWN first to observe living cells, including blood cells, sperm cells, bacteria, and single-celled organisms (algae and protozoa) found in pond water Brown found that every plant cell he looked at contained a rounded structure, which he called a nucleus, a term derived from the Latin word for “kernel.” Schleiden came to the important conclusion that all plant tissues are composed of cells and that an embryonic plant always arises from a single cell. The cell theory states that: Schwann postulate 1839 1. All organisms consist of one or more cells. 2. The cell is the basic unit of structure for all organisms. Virchow conclusion 1855 3. All cells arise only from preexisting cells. Cells exist in a wide variety of shapes and sizes A few examples of the diversity of cells that exist in our world.  Modern cell biology has come about by the interweaving of three historically distinct strands - cytology, biochemistry, and genetics - which in their early development probably did not seem at all related. The contemporary cell biologist must understand all three strands because they complement one another in the quest to learn what cells are made of and how they function. 1. THE CYTOLOGICAL STRAND DEALS WITH CELLULAR STRUCTURE The cytological strand is best studied using microscopes, which include both light and electron microscopy. The light microscope has allowed us to visualize individual cells, which are approximately 1-50 mm in size. Historically, its limited resolving power did not allow us to see details of structure smaller than about 0.2 mm (200 nm), but modern light microscopes are surpassing that limit. Several types of light microscopes allow us to view preserved or living specimens at magnifications of about 1000X. These include bright field, phase-contrast, differential interference contrast, fluorescence, confocal, and digital video microscopes, each of which offers particular advantages in studying and understanding cells. The electron microscope uses a beam of electrons, rather than visible light, for imaging specimens. It can magnify objects up to 100,000X with a resolving power of less than 1 nm, enabling us to view subcellular structures such as membranes, ribosomes, organelles, and even individual DNA and protein molecules. Most electron microscopes have one of two basic designs: the transmission electron microscope (TEM) and the scanning electron microscope (SEM). Transmission and scanning electron microscopes are similar in that each employs a beam of electrons, but they use quite different mechanisms to form the image. TEM forms an image from electrons that are transmitted through the specimen. A SEM, on the other hand, scans the surface of the specimen and forms an image by detecting electrons that are deflected from its outer surface. 2. THE BIOCHEMICAL STRAND CONCERNS THE CHEMISTRY OF BIOLOGICAL STRUCTURE AND FUNCTION Discoveries in biochemistry have revealed how many of the chemical processes in cells are carried out, greatly expanding our knowledge of how cells function. Biochemistry's impact on understanding cellular processes. Friedrich Wöhler's revolutionary discovery in 1828. Wöhler revolutionized our thinking about biology and chemistry by demonstrating that urea, an organic compound of biological origin, could be synthesized in the laboratory from an inorganic starting material, ammonium cyanate Transition from biological uniqueness to chemical principles. Major discoveries in biochemistry were the identification of enzymes as biological catalysts, the discovery of adenosine triphosphate (ATP) as the main carrier of energy in living organisms, the description of the major metabolic pathways cells use to harness energy and synthesize cellular components. Biochemistry took another major step forward with the development of techniques for isolating, purifying, and analyzing subcomponents of cells. Centrifugation is a means of separating and isolating subcellular structures and macromolecules based on their size, shape, and/or density—a process called subcellular fractionation. Especially useful for resolving small organelles and macromolecules is the ultracentrifuge, developed by Swedish chemist Theodor Svedberg in the late 1920s. An ultracentrifuge is capable of very high speeds - more than 100,000 revolutions per minute - and can thereby subject samples to forces exceeding 500,000 times the force of gravity Other biochemical techniques that have proven useful for separating and purifying subcellular components include chromatography and electrophoresis. Chromatography is a general term describing a variety of techniques by which a mixture of molecules in solution is separated into individual components. Electrophoresis refers to several related techniques that use an electrical field to separate macromolecules based on their mobility through a semisolid gel. 3. THE GENETIC STRAND FOCUSES ON INFORMATION FLOW Gregor Mendel's groundbreaking work in the genetic strand commenced with his iconic experiments involving pea plants in a monastery garden. His 1866 publication introduced the principles of segregation and independent assortment of genes, termed "hereditary factors." In 1880, German biologist Walther Flemming identified chromosomes, threadlike bodies seen in dividing cells. Flemming called the division process mitosis, from the Greek word for “thread.” Chromosome number soon came to be recognized as a distinctive characteristic of a species and was shown to remain constant from generation to generation. The chromosome theory of heredity states that the characteristics of organisms passed down from generation to generation result from the inheritance of chromosomes carrying discrete physical units known as genes. Each gene is a specific sequence of DNA that contains the information to direct the synthesis of one cellular protein. DNA itself is a double helix of complementary strands held together by precise base pairing. This structure allows the DNA to be accurately duplicated as it is passed down to successive generations. The flow of genetic information in cells is typically from DNA to RNA to protein, although exceptions such as reverse transcription exist. Expression of this genetic information to produce a protein requires several important types of RNA: mRNA, tRNA, and rRNA. Current understanding of gene expression has relied heavily on the development of recombinant DNA technology since the 1970s. This technology was made possible by the discovery of restriction enzymes, which have the ability to cleave DNA molecules at specific sequences so that scientists can create recombinant DNA molecules containing DNA sequences from two different sources. The technology led quickly to the development of DNA cloning, a process used to generate many copies of specific DNA sequences for detailed study and further manipulation; and DNA transformation, the process of introducing DNA into cells. DNA sequencing methods were devised for rapidly determining the base sequences of DNA molecules. This technology is now routinely applied not just to individual genes but also to entire genomes. Bioinformatics and “–Omics.” The challenge of analyzing the vast amount of data generated by DNA sequencing has led to a new discipline, called bioinformatics, which merges computer science and biology as a means of making sense of sequence data. Bioinformatics allows us to compare and analyze thousands of genes or other molecules simultaneously, causing a revolution in genomic, proteomic, and numerous other fields of “–omics” research. CRISPR genome editing is an exciting new technique that allows precise changes to genomic sequences. clustered regularly interspaced short palindromic repeats – is a family of DNA sequences found in the genome of prokaryotics. Scientists have developed a number of model systems to study cellular processes directly in living cells and organisms. Cell and Tissue Cultures. Scientists make extensive use of cell cultures as model systems. Many types of cells can be grown in the laboratory outside their tissue of origin - such as skin cells, muscle cells, and cancer cells. Some of the first human cells ever grown in defined culture conditions in the laboratory were HeLa cells taken from cervical cancer tissue obtained from a woman named Henrietta Lacks in 1951. Descendants of her cells are still being grown today and are commonly used in cancer and virus research. Model Organisms. A model organism is a species that is widely studied, well characterized, and easy to manipulate and has particular advantages, making it useful for experimental studies. A few examples are the bacterium Escherichia coli, the yeast Saccharomyces cerevisiae, and the fruit fly Drosophila melanogaster. Similarly, C. elegans is a widely used model organism for studies of cell differentiation and development in multicellular organisms. For studies of cellular and physiological processes specific to mammals (including humans), the common laboratory mouse (Mus musculus) has become the primary model organism. It shares many cellular, anatomical, and physiological similarities with humans and is widely used for research in medicine, immunology, and aging. For flowering plant studies, Arabidopsis thaliana is a powerful model organism. It has one of the smallest genomes of any plant and a rapid (6-week) life cycle, facilitating genetic studies.